Journal Article
. 2012 Jul; 8319:.

Managing and Querying Whole Slide Images

Fusheng Wang 1 Tae W Oh  Cristobal Vergara-Niedermayr  Tahsin Kurc  Joel Saltz  
Affiliations
  • PMID: 22844574
  •     7 References
  •     7 citations

Abstract

High-resolution pathology images provide rich information about the morphological and functional characteristics of biological systems, and are transforming the field of pathology into a new era. To facilitate the use of digital pathology imaging for biomedical research and clinical diagnosis, it is essential to manage and query both whole slide images (WSI) and analytical results generated from images, such as annotations made by humans and computed features and classifications made by computer algorithms. There are unique requirements on modeling, managing and querying whole slide images, including compatibility with standards, scalability, support of image queries at multiple granularities, and support of integrated queries between images and derived results from the images. In this paper, we present our work on developing the Pathology Image Database System (PIDB), which is a standard oriented image database to support retrieval of images, tiles, regions and analytical results, image visualization and experiment management through a unified interface and architecture. The system is deployed for managing and querying whole slide images for In Silico brain tumor studies at Emory University. PIDB is generic and open source, and can be easily used to support other biomedical research projects. It has the potential to be integrated into a Picture Archiving and Communications System (PACS) with powerful query capabilities to support pathology imaging.

Other Links

Free PMC article 
In silico analysis of nuclei in glioblastoma using large-scale microscopy images improves prediction of treatment response.
Jun Kong, Lee Cooper, +4 authors, Daniel Brat.
Annu Int Conf IEEE Eng Med Biol Soc, 2012 Jan 19; 2011. PMID: 22254257    Free PMC article.
A data model and database for high-resolution pathology analytical image informatics.
Fusheng Wang, Jun Kong, +10 authors, Joel Saltz.
J Pathol Inform, 2011 Aug 17; 2. PMID: 21845230    Free PMC article.
The cell centered database project: an update on building community resources for managing and sharing 3D imaging data.
Maryann E Martone, Joshua Tran, +6 authors, Mark H Ellisman.
J Struct Biol, 2007 Dec 07; 161(3). PMID: 18054501    Free PMC article.
An integrative approach for in silico glioma research.
Lee A D Cooper, Jun Kong, +13 authors, Joel H Saltz.
IEEE Trans Biomed Eng, 2010 Jul 27; 57(10). PMID: 20656651    Free PMC article.
The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.
Ilya G Goldberg, Chris Allan, +7 authors, Jason R Swedlow.
Genome Biol, 2005 May 17; 6(5). PMID: 15892875    Free PMC article.
ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology.
David J Foran, Lin Yang, +8 authors, Joel H Saltz.
J Am Med Inform Assoc, 2011 May 25; 18(4). PMID: 21606133    Free PMC article.
Integrated morphologic analysis for the identification and characterization of disease subtypes.
Lee A D Cooper, Jun Kong, +12 authors, Joel H Saltz.
J Am Med Inform Assoc, 2012 Jan 27; 19(2). PMID: 22278382    Free PMC article.
Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data.
David A Gutman, Jake Cobb, +6 authors, Lee A D Cooper.
J Am Med Inform Assoc, 2013 Jul 31; 20(6). PMID: 23893318    Free PMC article.
OpenSlide: A vendor-neutral software foundation for digital pathology.
Adam Goode, Benjamin Gilbert, +2 authors, Mahadev Satyanarayanan.
J Pathol Inform, 2013 Nov 19; 4. PMID: 24244884    Free PMC article.
Image Montaging for Creating a Virtual Pathology Slide: An Innovative and Economical Tool to Obtain a Whole Slide Image.
Spoorthi Ravi Banavar, Prashanthi Chippagiri, +2 authors, Premalatha Bidadi Rajashekaraiah.
Anal Cell Pathol (Amst), 2016 Oct 18; 2016. PMID: 27747147    Free PMC article.
Enhancing the Value of Histopathological Assessment of Allograft Biopsy Monitoring.
Michelle A Wood-Trageser, Andrew J Lesniak, Anthony J Demetris.
Transplantation, 2019 Feb 16; 103(7). PMID: 30768568    Free PMC article.
Review.
MaReIA: A Cloud MapReduce Based High Performance Whole Slide Image Analysis Framework.
Hoang Vo, Jun Kong, +4 authors, Fusheng Wang.
Distrib Parallel Databases, 2019 Jun 21; 37(2). PMID: 31217669    Free PMC article.
piNET-An Automated Proliferation Index Calculator Framework for Ki67 Breast Cancer Images.
Rokshana Stephny Geread, Abishika Sivanandarajah, +4 authors, April Khademi.
Cancers (Basel), 2020 Dec 31; 13(1). PMID: 33375043    Free PMC article.
Neuroblastoma GD2 Expression and Computational Analysis of Aptamer-Based Bioaffinity Targeting.
Godfred O Sabbih, Michael K Danquah.
Int J Mol Sci, 2021 Aug 28; 22(16). PMID: 34445807    Free PMC article.
Review.